Dear Ananya,
Shouldn't this be something you already had in mind even before attempting
to simulate? Usually, a simulation is a means to an end. What is your end,
ie. what made you do this simulation? The motivation behind your simulation
is usually what will determine what type of validation it r
On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote:
Dear Ananya,
Shouldn't this be something you already had in mind even before
attempting
to simulate? Usually, a simulation is a means to an end. What is your
end,
ie. what made you do this simulation? The motivation behind your
simulat
Dear Ananya,
Sorry but I don't understand what you're saying. What do you mean by "molecular
movement of my protein"? Do you mean diffusion? Please be more specific.
You also mention "authenticity", but I don't think that's what you meant...
You have done PCA, RMSD and RMSF analyses. That's nice
Helllo all!
In my general situation, I have a batch of homology models that I would like
to assess for stability by molecular dynamics.
I am working with a postdoc in my lab who was extensive experience with
NAMD, but does not use GROMACS. We have been developing protocol for these
MD simulation
Dear Sir,
My protein contains two domain and upon GTP hydrolysis, the protein
under goes conformational change and it shows inter-domain movement. I
did few biochemical test which showed me that the upon a mutation in the
conserved residue (which is localed in the chain connecting the two
dom
First of all, please address me in a casual manner, "Sir" makes me feel old
and I'm just in my mid 20's :)
Now I'll try to be as less verbose as I can, because I think there's a
little communication issue here.
Authenticity usually points out towards originality, something not copied,
genuine. I
On Tue, Feb 11, 2014 at 6:12 AM, Chaitali Chandratre
wrote:
> Dear Sir,
>
> Below is error message for gromacs-4.6.4 gpu enabled install:
> ---
> make error :
>
> "[chaitalij@gpu
On Tue, Feb 11, 2014 at 12:11 PM, unitALX wrote:
> Helllo all!
>
> In my general situation, I have a batch of homology models that I would like
> to assess for stability by molecular dynamics.
>
> I am working with a postdoc in my lab who was extensive experience with
> NAMD, but does not use GROM
hi GMX users
i want to use AMBER03 force field for protein-ligand complex simulation. can
i use antechamber for the particle charges of the ligand or i must to use
b3lyp/cc-pVTZ calculation in an implicit solvent model?
thanks for your help
--
Gromacs Users mailing list
* Please search the ar
Hi Ananya,
You have several options to validate the results you have
1. Perform the simulations again
2. Apply the reverse mutations and simulate again
3. Perform (covariance) analysis on different blocks
4. Extract a measurable property and compare it to experiments
ad 1.:
Redoing the simulati
Hehe that is a good point!
Indeed, he says that multiple time stepping is a better compromise on
increasing speed. However, he says the NAMD multiple step scheme uses 4fs
for long range electrostatics, while using 1fs for bonded interactions. So
actually, the theoretical root of the disagreement se
Hi,
Personally I would also ask your colleague if he could also provide evidence
(e.g. published papers) to back up what he is saying to you (i.e. that it is
necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable
results). This way, you can make an informed decision based u
Hello,
I found the following posts in the forum related to g_enemat problems:
(A) year 2001 post:
http://gromacs.5086.x6.nabble.com/using-g-enemat-td4391042.html
(B) year 2013 post:
http://gromacs.5086.x6.nabble.com/interaction-energy-using-g-enemat-td5010085.html
In this post, Justin mention
On 2/11/14, 10:09 AM, shivangi nangia wrote:
Hello,
I found the following posts in the forum related to g_enemat problems:
(A) year 2001 post:
http://gromacs.5086.x6.nabble.com/using-g-enemat-td4391042.html
(B) year 2013 post:
http://gromacs.5086.x6.nabble.com/interaction-energy-using-g-e
Hi Ananya,
I have TWO suggestions as to how you could further validate your simulation:
(1) Repeat the same simulation in an exactly similar manner but using other
force fields. For example,
do you reproduce similar MD profile if you use CHARMM force field in lieu
of AMBER or vice versa. If yes,
Yar, I understand. However, because of the differences in software
experience (NAMD / GROMACS), presenting literature references is not as
effective as I thought it would be, historical inertia and spirited
argumentation is having more weight than I thought it would, and in between
what is publishe
Well,
I also would check which kind of movements I am looking for. It is a known
fact that some domain (and, thereby, larger) movements occur in larger
timescales and that might not be your case.
E.g: you are expecting to see major movements in nanoseconds timescale.
I hope this helps.
Best reg
On 2/11/14, 6:43 AM, ananyachatterjee wrote:
Dear Sir,
My protein contains two domain and upon GTP hydrolysis, the protein under goes
conformational change and it shows inter-domain movement. I did few biochemical
test which showed me that the upon a mutation in the conserved residue (which is
Hi,
Now I am studying the aggregation propensity of a peptide using
gromacs. To study the effect of neighbouring molecules on aggregation I am
planning to do an MD simulation by reducing distance between end of the
protein and edge of the box. Is this is physically significant? Then what
is
On 2/11/14, 1:59 PM, Shine A wrote:
Hi,
Now I am studying the aggregation propensity of a peptide using
gromacs. To study the effect of neighbouring molecules on aggregation I am
planning to do an MD simulation by reducing distance between end of the
protein and edge of the box. Is thi
Hi, I'm not a Biologist, I'm designer interested to molecular modelling and
3D visualization of proteins and molcules.
I use gromacs but I'm not an expert of this.
I would create an animation of the interaction between D-Alanyl -D Alanine
carboxypeptidase and penicillin. In general i would see how
You should take a look at this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
Best,
Aldo
===
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blo
Hi,
For your problem of assessing a homology model, I think that there are
lots of other issues that I would be far more concerned about (e.g.
force field accuracy, convergence of your simulations, etc.). To be
fairly sure of anything I see in a simulation, I ideally would like to
observe the
On Tue, Feb 11, 2014 at 12:11 PM, unitALX wrote:
>
> Helllo all!
>
> In my general situation, I have a batch of homology models that I would
like
> to assess for stability by molecular dynamics.
>
> I am working with a postdoc in my lab who was extensive experience with
> NAMD, but does not use GR
On 2/11/14, 2:48 PM, Aldo Segura wrote:
You should take a look at this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
It's worth noting that while what the OP is trying to can be accomplished using
SMD, the time investment would be quit
Hi Andrea!!!
Can you please help me by sending the tool you mentioned! I'm working on
similar thing and need to calculate the binding energies.
email: richa.s.rath...@gmail.com
It would be great help!
Thanks and regards
Richa
--
View this message in context:
http://gromacs.5086.x6.nabble.com/M
Dear GMX users:
I am fairly new to gromacs. I am trying to simulate SWM4 water model. In
the model the electrostatic interactions between the Drude particle (DOH2)
and oxygen atom (OP) are excluded. I have created an index file index.ndx
that contains the numbers of the DOH2 and OP atoms. In the g
Hi Justin.
I hope you have a nice day
I would like to simulate a peptide on the membrane .In tutorial gromacs that
simulate peptide KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I
need to do this step for my system?
May you can help me؟
Thanks
--
Gromacs Users mailing list
* P
28 matches
Mail list logo
